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Due to Finland's geographical location and settlement history, the country has been a genetic isolate. Contemporary studies show that genetic diversity is still slightly reduced among the Finnish population, especially in the eastern part of the country and in males. This diversity reduction and the specific 'Finnish Disease Heritage' could be explained by founder effects and bottlenecks. Archaeologically, there is evidence for fluctuation of population size, including bottlenecks at 4100-3800 BP and 1500-1300 BP.Together with population size estimates based on archaeological data, we use methods and ideas from genetics in order to assess the existence and size of possible prehistoric population bottlenecks. Well-preserved ancient organic remains providing aDNA are practically non-existent in Finland due to the naturally acidic soil. Thus, we employ population simulations to follow genetic changes over hundreds of generations and evaluate the effects of a Neolithic population bottleneck on the past and present Finnish gene pool, with archaeologically justified population size changes. Here, in continuation of our previous research, we apply forward simulations with mtDNA and Y chromosomal haplotypes to trace back possible population histories behind the present day genetic diversity in Finland. The simulations were carried out with the population genetic simulation environment simuPOP.Our model simulation begins at 11,000 BP when the first pioneers settled the country after the last Ice Age. The prehistoric Finnish population is simulated with two archaeologically justified bottlenecks. We split the population into geographic sub-populations, added gender-specific migration as well as migration waves from neighbouring populations, compatible with archaeological phenomena. To follow the assumed demographic events as realistically as possible, we added minor constant gene flow from three background populations: Archaic European, Archaic Scandinavian and Saami. The mtDNA frequencies of the background populations have been assigned according to actual ancient mtDNA haplotype frequencies acquired from published aDNA studies of prehistoric European populations.The preliminary results indicate, as expected, that bottlenecks substantially reduce genetic diversity, at least with the narrowest bottlenecks. Furthermore, a surprisingly small constant gene flow from neighbouring populations clearly outweighs the effects of larger, short-term migration waves. Interestingly, bottleneck severity has a smaller effect on Y-STR than mitochondrial haplotype diversity in these simulations. Compared with our previous simulations, the gender-specific migration brings the simulated genetic diversity closer to the observed contemporary genetic diversity in Finland, especially in the narrowest bottleneck models. A genetic simulation approach enables us to exclude the least compatible scenarios when modelling past demographic events.